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LOCUS JX446725 5057 bp RNA linear VRL 12-OCT-2012
DEFINITION HIV-1 isolate AA005a03L from Thailand gag protein (gag) gene,
complete cds; pol protein (pol) gene, partial cds; and vif protein
(vif) and vpr protein (vpr) genes, complete cds
ACCESSION JX446725
VERSION JX446725.1 GI:407732208
KEYWORDS .
SOURCE Human immunodeficiency virus 1 (HIV-1)
ORGANISM Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
group
REFERENCE 1 (bases 1 to 5057)
Show all sequences for reference 1
AUTHORS Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
Sanders-Buell,E., Hertz,T., deCamp,A.C., Carrico,C., Menis,S.,
Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J.,
deSouza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
TITLE Increased HIV-1 vaccine efficacy against viruses with genetic
signatures in Env V2.
JOURNAL Nature.. 490(7420); 417-20 (2012)
PUBMED 22960785
REFERENCE 2 (bases 1 to 5057)
Show all sequences for reference 2
AUTHORS Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
Sanders-Buell,E., Hertz,T., de Camp,A.C., Carrico,C., Menis,S.,
Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J., de
Souza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
TITLE Direct Submission
JOURNAL Submitted (01-AUG-2012) US Military HIV Research Program, 503
Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT ##Assembly-Data-START## Sequencing Technology Sanger dideoxy
sequencing ##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..5057
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="AA005a03L"
/isolation_source="plasma AA005a"
/host="Homo sapiens; RV144 trial participant AA005"
/db_xref="taxon:11676"
/country="Thailand"
/collection_date="2007"
/note="subtype: CRF01_AE"
gene 2..1498
/gene="gag"
CDS 2..1498
/gene="gag"
/codon_start="1"
/transl_table="1"
/product="gag protein"
/protein_id="AFU26148.1"
/db_xref="GI:407732209"
/translation="MGARASVLTGGKLDAWEKIRLRPGGKKKYRIKHLVWASRELERF
ALNPGLLETSEGCQQIIEQLQSTLKTGSEELKSLYNAVATLWCVHQRIDVKDTKEALD
KMEEAQKRSQQKTQQAAAGTGSSSKVSQNYPIVQNAQGQMVHQSLSPRTLNAWVKVVE
EKGFNPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKETINEEAAEWDRVHPV
HAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRM
YSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKSIL
KALGTGATLEEMMTACQGVGGPSHKARVLAEAMSQAQNVNIMMQRGNFKGQKRIKCFN
CGKEGHLARNCRAPRKRGCWKCGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSR
PEPSAPPAENWGMGEETPSLLKQEQKDREHPPPSVSLKSLFGNDPLSQ"
misc_feature 5..>334
/gene="gag"
/note="gag gene protein p17 (matrix protein); Region:
Gag_p17; pfam00540"
/db_xref="CDD:109591"
misc_feature 446..1090
/gene="gag"
/note="gag gene protein p24 (core nucleocapsid protein);
Region: Gag_p24; pfam00607"
/db_xref="CDD:201337"
misc_feature 1163..1216
/gene="gag"
/note="Zinc knuckle; Region: zf-CCHC; pfam00098"
/db_xref="CDD:189387"
misc_feature 1226..1279
/gene="gag"
/note="Zinc knuckle; Region: zf-CCHC; pfam00098"
/db_xref="CDD:189387"
misc_feature 1340..1447
/gene="gag"
/note="Gag protein p6; Region: Gag_p6; pfam08705"
/db_xref="CDD:149684"
gene <1291..4302
/gene="pol"
CDS <1291..4302
/gene="pol"
/codon_start="1"
/transl_table="1"
/product="pol protein"
/protein_id="AFU26149.1"
/db_xref="GI:407732210"
/translation="FFRENLAFQQRKAREFSSEQTRAISPTSRKLGDGGRDTFLAEAG
AERQGTPSSFSFPQITLWQRPLVTVKIGGQLREALLDTGADDTVLEEINLPGKWKPKM
IGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNMLTQIGCTLNFPISPI
DTVPVTLKPGMDGPKVKQWPLTEEKIKALTEICKEMEEEGKISKIGPENPYNTPIFAI
KKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLD
ESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPEIV
IYQYMDDLYVGSDLEIGQHRTKVEELRAHLLSWGFTTPDKKHQKEPPFLWMGYELHPD
KWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYPGIKVKQLCRLLRGAKALTDIVPL
TEEAELELAENREILKTPVHGVYYDPSKDLIAEVQKQGQDQWTYQIYQEPFKNLKTGK
YARKRSTHTNDVRQLAEAVQKIATESIVIWGKTPKFKLPIQRETWETWWMEYWQATWI
PEWEFVNTPPLVKLWYQLEKDPIVGAETFYVDGAASRETKLGKAGYVTDRGRQKVVSL
TETTNQKTELQAIHLALQDSGSEVNIVTDSQYALGIIQAQPDRSESEVVNQIIEDLIK
KEKVYLSWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEEHERYHSNWRTMASD
FNLPPIVAKEIVASCDKCQLKGEALHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGY
IEAEVIPAETGHETAYFLLKLAGRWPVKVVHTDNGSNFTSAAVKAACWWANIKQEFGI
PYNPQSQGVVESMNKELKKIIGQIRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGER
IIDIIATDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDI
KVVPRRKAKIIRDYGKQMAGDDCVAGRQDED"
misc_feature 1489..1731
/gene="pol"
/note="Retropepsins, pepsin-like aspartate proteases;
Region: HIV_retropepsin_like; cd05482"
/db_xref="CDD:133149"
misc_feature order(1531..1533,1537..1539,1543..1545,1594..1602,1708..17
10)
/gene="pol"
/note="inhibitor binding site; inhibition site"
/db_xref="CDD:133149"
misc_feature 1531..1539
/gene="pol"
/note="catalytic motif [active]"
/db_xref="CDD:133149"
misc_feature 1531..1533
/gene="pol"
/note="Catalytic residue [active]"
/db_xref="CDD:133149"
misc_feature order(1594..1608,1612..1626)
/gene="pol"
/note="Active site flap [active]"
/db_xref="CDD:133149"
misc_feature 1807..2457
/gene="pol"
/note="RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and...;
Region: RT_Rtv; cd01645"
/db_xref="CDD:73152"
misc_feature order(1825..1830,1936..1938,1948..1950,1969..1971,1975..19
83,1987..1989,1996..1998,2020..2022,2026..2031,2035..2037,
2083..2100,2206..2211,2215..2217,2224..2226,2302..2304,230
8..2313,2443..2448)
/gene="pol"
/note="active site"
/db_xref="CDD:73152"
misc_feature order(1825..1830,1975..1983,1987..1989,1996..1998,2020..20
22,2026..2031,2035..2037,2209..2211,2215..2217,2224..2226,
2302..2304,2443..2448)
/gene="pol"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:73152"
misc_feature 1942..2457
/gene="pol"
/note="Reverse transcriptase (RNA-dependent DNA
polymerase); Region: RVT_1; pfam00078"
/db_xref="CDD:200982"
misc_feature order(1948..1950,1969..1971,2083..2100,2206..2208,2308..23
10)
/gene="pol"
/note="dNTP binding site [chemical binding]; other site"
/db_xref="CDD:73152"
misc_feature order(2053..2064,2290..2292,2296..2298,2317..2319,2323..23
25,2434..2436)
/gene="pol"
/note="NNRTI binding site; other site"
/db_xref="CDD:73152"
misc_feature 2467..2676
/gene="pol"
/note="Reverse transcriptase thumb domain; Region:
RVT_thumb; pfam06817"
/db_xref="CDD:115473"
misc_feature 2704..3012
/gene="pol"
/note="Reverse transcriptase connection domain; Region:
RVT_connect; pfam06815"
/db_xref="CDD:203523"
misc_feature 3070..3408
/gene="pol"
/note="non-LTR RNase HI domain of reverse transcriptases;
Region: Rnase_HI_RT_non_LTR; cd09276"
/db_xref="CDD:187700"
misc_feature order(3082..3084,3187..3189,3247..3249,3400..3402)
/gene="pol"
/note="active site"
/db_xref="CDD:187700"
misc_feature order(3082..3090,3094..3096,3172..3180,3187..3189,3247..32
49,3358..3360)
/gene="pol"
/note="RNA/DNA hybrid binding site [nucleotide binding];
other site"
/db_xref="CDD:187700"
misc_feature 3457..3576
/gene="pol"
/note="Integrase Zinc binding domain; Region:
Integrase_Zn; pfam02022"
/db_xref="CDD:202092"
misc_feature 3607..3921
/gene="pol"
/note="Integrase core domain; Region: rve; pfam00665"
/db_xref="CDD:201381"
misc_feature 4093..4245
/gene="pol"
/note="Integrase DNA binding domain; Region: IN_DBD_C;
pfam00552"
/db_xref="CDD:144223"
gene 4247..4825
/gene="vif"
CDS 4247..4825
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AFU26150.1"
/db_xref="GI:407732211"
/translation="MENRWQVMIVWQVDRMRIRTWHSLVKYHMYVSKKAKNWFYRHHY
ESQHPKVSSEVHIPIGEARLVVRTYWGLQTGEKAWQLGHGVSIEWRQGKYNTQVDPDL
ADQLIHLQYFDCFSDSAIRKAILGQVVRHRCEYPSGHNKVGSLQYLALKALTAPKRIK
PPLPSVKKLTEDRWNKPQKIRGHRENPTMNGH"
misc_feature 4247..4822
/gene="vif"
/note="Retroviral Vif (Viral infectivity) protein; Region:
Vif; pfam00559"
/db_xref="CDD:109609"
gene 4765..5055
/gene="vpr"
CDS 4765..5055
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AFU26151.1"
/db_xref="GI:407732212"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKNEAVRHFPRPWLHGLGQ
HIYNTYGDTWEGVEAIVRILHQLLFVHFRIGCQHSRIGIIPGRRGRNGAGRS"
misc_feature 4765..5001
/gene="vpr"
/note="VPR/VPX protein; Region: VPR; pfam00522"
/db_xref="CDD:109573"
BASE COUNT 1926 a 865 c 1191 g 1075 t
ORIGIN
1 gatgggtgcg agagcgtcag tattaactgg gggaaaatta gatgcatggg aaaaaattcg
61 gttgcggcca gggggaaaga aaaaatatag gataaaacat ttagtatggg caagcagaga
121 gttagaaaga tttgcactta accctggcct tttagaaaca tcagaaggat gtcaacagat
181 aatagaacag ttacaatcaa ctctcaagac aggatcagag gaacttaaat ctttatataa
241 tgcagtagca accctttggt gcgtacacca aagaatagat gtaaaagaca ccaaggaagc
301 tttagataaa atggaagaag cacaaaagag gagtcagcaa aagacacaac aggcagcagc
361 tggcacagga agcagcagca aagtcagcca aaattaccct atagtgcaaa atgcacaagg
421 gcaaatggta catcagtctt tatcacctag aactttgaat gcatgggtaa aagtagtaga
481 agaaaagggt tttaaccctg aagtaatacc catgttctca gcattatcag agggagccac
541 cccacaagat ttaaatatga tgctaaatat agtgggagga caccaggcag caatgcaaat
601 gttaaaagaa accatcaatg aggaagctgc agaatgggat agggtacacc cagtacatgc
661 agggccgatt ccaccaggcc agatgaggga accaagggga agtgacatag caggaactac
721 tagtaccctt caagaacaaa taggatggat gacaagcaat ccacctatcc cagtgggaga
781 tatctataaa aggtggataa tcctgggatt aaataaaata gtaagaatgt atagccctgt
841 tagcattttg gacataagac aagggccaaa agaacccttc agagactatg tagataggtt
901 ctataagact ctcagagcag aacaagctac acaggaggta aagaattgga tgacagaaac
961 cttgctagtc caaaatgcga atccagactg taaatccatc ttaaaagcat taggaacagg
1021 agctacatta gaagagatga tgacagcatg tcagggagtg ggaggaccta gccataaagc
1081 aagggttttg gctgaggcaa tgagccaagc acaaaatgta aatataatga tgcagagagg
1141 caactttaag ggccagaaaa gaattaagtg cttcaactgt ggcaaagaag ggcacctagc
1201 cagaaattgc agggccccta gaaaaagggg ttgttggaaa tgtggaaagg aaggacatca
1261 aatgaaagac tgcactgaga gacaggctaa ttttttaggg aaaatctggc cttccaacaa
1321 aggaaggcca gggaattttc ctcagagcag accagagcca tcagccccac cagcagaaaa
1381 ctgggggatg ggggaagaga caccttcctt gctgaagcag gagcagaaag acagggaaca
1441 ccctcctcct tcagtttccc tcaaatcact ctttggcaac gaccccttgt cacagtaaaa
1501 ataggaggac aactaagaga agctctatta gatacaggag cagatgatac agtattagaa
1561 gaaataaatt tgccaggaaa atggaaacca aaaatgatag ggggaattgg aggttttatc
1621 aaagtaaggc aatatgatca gatacttata gaaatttgtg gaaagaaggc tataggtaca
1681 gtgttagtag gacctacacc tgtcaacata attggacgaa atatgttgac tcagattggc
1741 tgtactttaa atttcccaat tagtcctatt gacactgtac cagtaacatt aaagccagga
1801 atggatggac caaaggttaa acaatggcca ttgacagaag aaaaaataaa agcattaaca
1861 gaaatttgta aagagatgga agaggaagga aaaatctcaa aaattgggcc tgaaaatcca
1921 tacaatactc caatatttgc tataaagaaa aaggacagca ccaagtggag gaaattagta
1981 gatttcagag agctcaataa aagaacacag gacttttggg aagttcaatt aggaatacca
2041 catccagcag gtttaaaaaa gaaaaaatca gtgacagtac tagatgtggg agatgcatat
2101 ttttcagttc ctttagatga aagctttaga aagtatactg catttaccat acctagtata
2161 aacaatgaaa caccaggaat tagatatcag tacaatgtgc tgccacaggg atggaaagga
2221 tcaccggcaa tattccagag tagcatgaca aaaatcttag agccctttag aataaaaaat
2281 ccagaaatag ttatctatca atacatggat gacttgtatg taggatctga tttagaaata
2341 gggcagcaca gaacaaaagt agaggagcta agagctcatc tattgagctg gggatttact
2401 acaccagaca aaaagcatca gaaggaacct ccattccttt ggatggggta tgagctccat
2461 cctgacaaat ggacagtcca gcctatagaa ctgccagaaa aagacagctg gactgtcaat
2521 gatatacaga aattagtggg aaagctaaat tgggcaagtc aaatttatcc agggattaag
2581 gtaaagcaac tgtgtagact cctcagggga gctaaagcac taacagacat agtaccactg
2641 actgaagaag cagaattaga attagcagag aacagggaga ttctaaaaac ccctgtgcat
2701 ggggtatatt atgacccatc aaaagactta atagcagaag tacagaaaca agggcaagac
2761 caatggacat atcaaattta tcaggagcca tttaaaaatc taaagacagg aaaatatgca
2821 agaaaaaggt ctactcacac taatgatgta agacaattag cagaagcggt gcaaaaaata
2881 gccacagaga gcatagtaat atggggaaag acccctaaat ttaaattgcc catacaaaga
2941 gagacatggg aaacatggtg gatggagtat tggcaagcta cctggattcc tgaatgggag
3001 tttgtcaata cccctcctct agtaaaatta tggtatcaat tagaaaagga ccccatagta
3061 ggagcagaga ctttctatgt agatggggca gctagtaggg agactaagct aggaaaagca
3121 ggatatgtca ctgacagagg aagacaaaag gtagtttccc taactgagac aacaaatcaa
3181 aagactgaat tacaagcgat ccatttagcc ttgcaggatt caggatcaga agtaaatata
3241 gtaacagact cacaatatgc attaggaatc attcaggcgc aaccagacag gagtgaatca
3301 gaagtagtca accaaataat agaggactta ataaaaaagg aaaaggtcta cctgtcatgg
3361 gtaccagcac acaaagggat tggaggaaat gaacaagtag ataaattagt cagttcagga
3421 atcaggaagg tgctcttttt agatggcata gataaggctc aagaagagca tgaaagatat
3481 cacagcaatt ggagaacaat ggctagtgat tttaatttgc cacctatagt agcaaaggag
3541 atagtagcca gctgtgataa atgtcagcta aaaggggaag ctctacatgg acaagtggac
3601 tgtagtccag gaatatggca attagattgc acacacctag aagggaaagt catcctggta
3661 gcagtccacg tggccagtgg atatatagaa gcagaagtta tcccagcaga aacagggcat
3721 gagacagcat actttctgct aaaattagca ggaagatggc cagtaaaagt agtacacact
3781 gacaatggta gcaatttcac cagcgctgca gttaaagcag cctgttggtg ggccaatatc
3841 aaacaggaat ttgggattcc ctacaatccc caaagtcaag gagtagtaga gtctatgaat
3901 aaagaattaa agaaaatcat aggacagata agagatcaag ctgaacatct taagacagca
3961 gtacaaatgg cagtattcat tcacaatttt aaaagaaaag gggggattgg ggggtacagt
4021 gcaggggaaa gaataataga cataatagca acagacatac aaactaaaga actacaaaaa
4081 caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga cccaatttgg
4141 aaaggaccag caaaactact ctggaaaggt gaaggggcag tagtaataca agacaatagt
4201 gatatcaaag tagtaccaag aagaaaagca aagatcatta gggattatgg aaaacagatg
4261 gcaggtgatg attgtgtggc aggtagacag gatgaggatt agaacatggc acagtttagt
4321 aaaatatcat atgtatgtct caaagaaagc taaaaattgg ttttatagac atcattatga
4381 aagccagcat ccaaaagtaa gttcagaagt acatatccca ataggagagg ccagattagt
4441 agtgagaaca tattggggtc tgcagacagg agaaaaggca tggcaattgg gtcatggagt
4501 ctccatagaa tggaggcagg gaaaatataa cacacaagtc gatcctgacc tagcagacca
4561 actgattcat ctacaatatt ttgactgttt ttcagactct gccataagga aagccatatt
4621 aggacaagta gttagacata ggtgtgaata tccatcagga cataataagg taggatccct
4681 acaatatttg gcactgaaag cattaacagc accaaaaagg ataaagccac ctctgcccag
4741 tgttaagaaa ttaacagaag atagatggaa caagccccag aagatcaggg gccacagaga
4801 gaaccctaca atgaatggac attagaactg ttagaggagc ttaaaaatga agctgttaga
4861 cattttccca gaccctggct ccatggctta ggacagcaca tttataacac ttatggggat
4921 acttgggaag gggttgaagc tatagtaaga atcttgcatc aactgctgtt tgttcatttc
4981 agaattgggt gtcaacatag cagaataggc attataccag ggagaagagg caggaatgga
5041 gccggtagat cctaacc
//
last modified: Tue May 31 10:56 2022